The pre-tensioners are connected to the stock seat buckle (from what I can see in the manual) and are probably not a big deal.

It's the passenger presence system and the seat belt alarms that worry me. If the passenger seat is removed and the presence system not engaged, then won't the passenger air bag not function? Also, won't the seat belt alarms go off? Maybe with the seats removed, these functions become defunct?

I have Kirkeys in my car. When I install them I first disconnect the battery (just in case) and reconnect after the OEM seats are out. When you first fire up the car, you get a "Service Airbag" warning on the dash, which goes away when you hit the stalk end. No seat belt chimes. I use TeamTech harnesses so I don't really care about the seat belt pretensioners. But there are no seat belt alarms going off as I drive. No idea if the air bag for the front passenger seat are armed or not - again, they are irrelevant in my setup because the passenger would never reach the airbag. Strapped in tight and far back from the dash.